May 2008 Commit Log

Number of Commits:
68
Number of Active Developers:
7
bloomquist 2008-05-31 12:16 Rev.: 910

The Newton-Raphson step in the Block Update Operator now throws an Operator Failed Exception rather than a runtime exception when it does not coverge in the specified number of steps. This allows BEAST to continue running even if the block-updater doesn't work occasionally.

47 lines of code changed in 1 file:

bloomquist 2008-05-30 12:56 Rev.: 909

Added a tracer class that does importance sampling for the gmrf fixed grid.

104 lines of code changed in 1 file:

rambaut 2008-05-30 00:40 Rev.: 908

Fixed <leafTrait> element in TreeModel. Used for extracting a single trait parameter for a leaf.

3 lines of code changed in 1 file:

rambaut 2008-05-30 00:25 Rev.: 907

Fixed <leafTrait> element in TreeModel. Used for extracting a single trait parameter for a leaf.

419 lines of code changed in 2 files:

jheled 2008-05-29 19:07 Rev.: 906

remove duplicate replaceParameter

48 lines of code changed in 1 file:

rambaut 2008-05-29 07:59 Rev.: 905

Another improvement in efficency.

67 lines of code changed in 1 file:

rambaut 2008-05-29 07:53 Rev.: 904

Improved the efficiency of CompatibilityStatistic enormously by using BitSets. Still very slow for large trees. This is because it does a full traversal of the tree for each test and for each nodes compares against the set of clades in the constraints tree (breaks out as soon as an incompatibility is found).

88 lines of code changed in 2 files:

bloomquist 2008-05-29 06:25 Rev.: 903

Just some minor fixes to the Fixed Grid logger. Checked on an example, checks out ok.

1 lines of code changed in 1 file:

rambaut 2008-05-29 02:18 Rev.: 902

Fixed a bug introduced into FlexibleNode.insertChild in a recent update (use of System.arrayCopy).

Also fixed another parser discrepancy in TreeModelParser.

1004 lines of code changed in 4 files:

rambaut 2008-05-28 23:55 Rev.: 901

Fixed a few bugs in the birth-death XML generation.

15 lines of code changed in 2 files:

bloomquist 2008-05-28 12:14 Rev.: 900

Added some extra features to the fixed grid logger.

56 lines of code changed in 1 file:

jheled 2008-05-28 09:51 Rev.: 899

Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers

Renamed getSocketChild

Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute

364 lines of code changed in 76 files:

jheled 2008-05-28 09:38 Rev.: 898

cleanup: remove spurios old comments

4 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-05-27 17:02 Rev.: 897

Some improvements for mixing with relaxed clock models

452 lines of code changed in 6 files:

rambaut 2008-05-27 11:38 Rev.: 896

Added a flag to TreeLikelihood to allow missing taxa (defaults to false so that missing taxa throw an exception). If true then missing taxa are given missing data at all sites.

455 lines of code changed in 7 files:

bloomquist 2008-05-27 06:56 Rev.: 895

Added the GMRFSkyrideFixedGridLogger that projects the skyride random grid onto a fixed grid. Had to add an extra method to GMRFSkyrideLikelihood too.

220 lines of code changed in 3 files:

rambaut 2008-05-27 04:12 Rev.: 894

Small fix to this: Added a tree compatibility statistic. This takes the current tree and a (presumably) less resolved tree and tests whether they are compatible. This allows us to test compatibility with a 'constraints' tree rather than doing lots of monophyly constraints.

10 lines of code changed in 1 file:

rambaut 2008-05-27 03:39 Rev.: 893

Added a tree compatibility statistic. This takes the current tree and a (presumably) less resolved tree and tests whether they are compatible. This allows us to test compatibility with a 'constraints' tree rather than doing lots of monophyly constraints.

205 lines of code changed in 3 files:

rambaut 2008-05-27 02:35 Rev.: 892

Made a small mistake in my last commit: Fixed a couple of parser definitions that were giving warnings of unrecognized elements (thanks, Joseph, for putting this checking in).

1 lines of code changed in 1 file:

rambaut 2008-05-27 01:42 Rev.: 891

Fixed a couple of parser definitions that were giving warnings of unrecognized elements (thanks, Joseph, for putting this checking in).

47 lines of code changed in 3 files:

msuchard 2008-05-25 10:59 Rev.: 890

Added option in ScaleOperator to update all dimensions independently and simultaneously. Takes care of a severe mixing problem Philippe is having with the discrete diffusion model. For geographies with > 10 or so locations, we need to consider rjMCMC to add/remove rates instead of SSVS.

444 lines of code changed in 3 files:

rambaut 2008-05-25 04:12 Rev.: 889

Fix to do lazy sampling of ancestral states.

15 lines of code changed in 1 file:

msuchard 2008-05-24 06:05 Rev.: 888

Fixed sync problem in AncestralState. Must be called getNodeCount # of times.

5 lines of code changed in 1 file:

msuchard 2008-05-24 05:49 Rev.: 887

Checking out the use of the diffusion model for univariate processes. Added testComparativeMethod.xml to this aim. There's a broken bit in the TreeModelParser -- does find leafTaxon traits like it used to. ????

542 lines of code changed in 4 files:

rambaut 2008-05-23 22:52 Rev.: 886

Updated Build number in BeastVersion

3 lines of code changed in 2 files:

jheled 2008-05-23 21:10 Rev.: 885

silly typo

1 lines of code changed in 1 file:

jheled 2008-05-23 19:10 Rev.: 884

Do not parse local elements declares by XML rules with global parsers.

Add checks for incorrect XML files. Issue warnings, but running with -strict makes them errors. Report unexpected elements, i.e. unused elements.

169 lines of code changed in 14 files:

jheled 2008-05-23 19:06 Rev.: 883

code cleanup

22 lines of code changed in 1 file:

jheled 2008-05-23 19:05 Rev.: 882

small cleanup

1 lines of code changed in 1 file:

jheled 2008-05-23 19:03 Rev.: 881

import optimize

4 lines of code changed in 1 file:

jheled 2008-05-23 19:02 Rev.: 880

comment

5 lines of code changed in 1 file:

jheled 2008-05-23 11:23 Rev.: 878

correct one possible bug from a warning, fix other warnings

15 lines of code changed in 1 file:

rambaut 2008-05-23 00:58 Rev.: 877

Fixed various sources of NEXUS tree files so that they automatically enclose taxon labels in quotes if they contain spaces or other problematic characters.

30 lines of code changed in 3 files:

jheled 2008-05-21 16:11 Rev.: 876

add option to condition analysis on number of changes

24 lines of code changed in 2 files:

jheled 2008-05-21 16:10 Rev.: 875

call finalize() of parent class

4 lines of code changed in 1 file:

jheled 2008-05-21 16:09 Rev.: 874

comment out unused code

2 lines of code changed in 1 file:

jheled 2008-05-21 16:09 Rev.: 873

add missing exception signature

1 lines of code changed in 1 file:

jheled 2008-05-21 16:07 Rev.: 872

TN93 (Tamura and Nei) substitution model

471 lines of code changed in 2 files:

rambaut 2008-05-17 03:09 Rev.: 871

Added a logger that logs an ancestral state reconstruction for a given MRCA.

138 lines of code changed in 2 files:

jheled 2008-05-16 22:35 Rev.: 870

Add output of coalecent bins

196 lines of code changed in 7 files:

jheled 2008-05-16 22:33 Rev.: 869

fix another case of a never reached print statment

18 lines of code changed in 1 file:

jheled 2008-05-16 22:32 Rev.: 868

readability

9 lines of code changed in 1 file:

rambaut 2008-05-16 21:49 Rev.: 867

Fixed the parser for differenceStatistic

13 lines of code changed in 2 files:

jheled 2008-05-12 10:29 Rev.: 865

import of deleted file

0 lines of code changed in 1 file:

alexei.drummond 2008-05-12 09:39 Rev.: 864

8 lines of code changed in 1 file:

alexei.drummond 2008-05-12 09:37 Rev.: 863

updated yule tests. Removed old birth death models

312 lines of code changed in 6 files:

jheled 2008-05-12 09:28 Rev.: 862

small cleanup

4 lines of code changed in 1 file:

jheled 2008-05-12 09:17 Rev.: 861

small cleanup

1 lines of code changed in 1 file:

jheled 2008-05-12 09:16 Rev.: 860

remove unused code

15 lines of code changed in 1 file:

jheled 2008-05-12 09:14 Rev.: 859

use midpoints option

38 lines of code changed in 3 files:

jheled 2008-05-12 09:13 Rev.: 858

birth death model

261 lines of code changed in 6 files:

jheled 2008-05-12 09:11 Rev.: 857

rename of class

348 lines of code changed in 2 files:

alexei.drummond 2008-05-12 09:04 Rev.: 856

updated to log trees in nexus

6 lines of code changed in 1 file:

jheled 2008-05-12 08:27 Rev.: 855

interface comments

20 lines of code changed in 1 file:

jheled 2008-05-12 08:05 Rev.: 854

code cleanup

43 lines of code changed in 2 files:

jheled 2008-05-12 08:04 Rev.: 853

java 5 loops

5 lines of code changed in 1 file:

jheled 2008-05-12 08:03 Rev.: 852

Call non-node specific function first, to allow it to do per-taxa preprocessing if required

3 lines of code changed in 1 file:

jheled 2008-05-12 08:01 Rev.: 851

code police (make variable local)

2 lines of code changed in 1 file:

jheled 2008-05-12 07:57 Rev.: 850

Comment out unused statments

3 lines of code changed in 1 file:

jheled 2008-05-12 07:54 Rev.: 849

spelling and stuff

5 lines of code changed in 1 file:

alexei.drummond 2008-05-11 15:56 Rev.: 848

Some early code of Marc's before he knew what he was doing ;-) removed with his blessing.

0 lines of code changed in 1 file:

jheled 2008-05-10 20:14 Rev.: 847

MIssing attribute specification

2 lines of code changed in 1 file:

jheled 2008-05-10 20:13 Rev.: 846

Simple expression statistic (RPN based)

272 lines of code changed in 3 files:

rambaut 2008-05-08 23:09 Rev.: 845

toString() now calls getLogLikelihood to properly evalute the likelihood (previously only return the value of 'logLikelihood' which may not have been calculated). This will probably only be called when a treeLikelihood is put in a <report> element in the XML as it is used in testLikelihood.xml to check treeLikelihood give similar values to PAUP.

1 lines of code changed in 1 file:

jheled 2008-05-08 14:16 Rev.: 844

New birth death model conditioned on # taxa

122 lines of code changed in 2 files:

rambaut 2008-05-03 14:12 Rev.: 843

Fixed bug in TreeAnnotator where it was writing all posterior probabilities as zero.

9 lines of code changed in 1 file:

benjamin.redelings 2008-05-03 07:28 Rev.: 842

[FIX] Enable compilation using 'ant'

* build.xml: update lib/* elements
* build_release.xml: ditto.

8 lines of code changed in 2 files:

msuchard 2008-05-03 07:08 Rev.: 841

Did not mean to commit latest changes to RandomWalkOnMapOperator because they depend on many other changes that I have not yet debugged.

13 lines of code changed in 1 file:

April 2008 »

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